title: Chimpanzee cerebellum, biological rep 3

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Human Exon 1.0 ST Arrays (exon arrays) according to manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility.

scan_protocol: Hybridized Affymetrix Human Exon 1.0 ST Arrays (exon arrays) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility.

data_processing: Raw image files were processed using Affymetrix GCOS software to generate CEL data files. The GeneBASE algorithm (Kapur et al., 2007, Genome Biol 8:R82) was used to produce the expression values, with minor modifications. Exon array expression indexes were calculated by the JETTA program using perfect-match probes shared between human and chimpanzee genomes.

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).  Ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01).

value: cerebellum, Gender:male, Age:30 years


title: Chimpanzee liver, biological rep 2

status: Public on May 05 2009

type: RNA

city: Iowa City

first: Yi

last: Xing

state: IA

address: 3294 CBRB, 285 Newton Rd

department: Internal Medicine, Biomedical Engineering

country: USA

institute: University of Iowa

label: biotin

molecule: total RNA

organism: Pan troglodytes

source_name: chimpanzee liver

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).

tag: tissue

value: liver, Gender:male, Age:37 years


title: Chimpanzee liver, biological rep 1

value: liver, Gender:female, Age:27 years


title: Chimpanzee cerebellum, biological rep 2

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Human Exon Junction arrays (HJAY arrays) according to manufacturer’s protocols at the University of Iowa DNA facility.

scan_protocol: Hybridized Affymetrix Human Exon Junction arrays (HJAY arrays) were scanned following the manufacturer’s protocols at the University of Iowa DNA facility.

data_processing: Raw image files were processed using Affymetrix GCOS software to generate CEL data files. The GeneBASE algorithm (Kapur et al., 2007, Genome Biol 8:R82) was used to produce the expression values, with minor modifications. Exon array expression indexes were calculated by the JETTA program using perfect-match probes shared between human, chimpanzee and rhesus macaque genomes.

source_name: chimpanzee cerebellum

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix Human Exon Junction arrays (HJAY arrays) was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854).  Ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01).

value: cerebellum

tag: gender

value: male

tag: age

value: 37 years


title: 13190060 - seT48 vs pBINT48

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Effects of deregulation of a lipid acyl hydrolase gene (PLP2, At2g26560) on global transcriptome upon infection by Botrytis cinerea. This deregulation affects resistance levels against fungal and bacterial pathogens, likely by perturbing the biosynthesis of oxylipins. Oxylipins are fatty acid-derived compounds (example:jasmonic acid) with diverse signaling or antimicrobial properties.

hyb_protocol: pBINT48 Cy5 / seT48 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: leaf - media : soil hygrometry : 70% temperature : 20°C light : 12/12h

treatment_protocol: Name:Botrytis cinerea infection - time course study - pathogen infection,botrytis cinerea:time 0hour .

tag: strain

value: arabidopsis thaliana (columbia)

value: 7weekdev.stage (Boyes et al. Plant Cell 2001):boyes:5.10

value: arabidopsis thaliana (columbia)  mutant (seplp2:PLP2-overexpressor)


title: STAT3-/- MEF cell line 03

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: Spontaneously immortalized STAT3-/- MEFs were grown in DMEM supplemented with 10% heat-inactivated FCS, 2 mM L-glutamine, 100 U/ml of penicillin, 100 μg/ml of streptomycin and maintained at 37°C in a 5% CO2 atmosphere. Cells were treated with Oncostatin M (OSM) (R&D Systems Inc.) at a final concentration of 20 ng/ml for 30 minutes.

hyb_protocol: cRNA was hybridized on MGU74A v2 Affymetrix DNA chip according to the Affymetrix protocol.

scan_protocol: The chip was scanned with Affymetrix scanner, using default parameters.

data_processing: Microarray quality control and feature selection was done using Bioconductor . The presence of hybridization/construction artifacts was evaluated with the fitPLM function (Bioconductor package affyPLM). The probes (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by mean of GCRMA (Bioconductor package gcrma), and normalization was done according to quantiles method.

organism: Mus musculus

source_name: MEF cell line

label_protocol: cRNA was generated according to the Affymetrix protocol.

extract_protocol: Total RNA was extracted and purified from cell lines using the Quiagen RNeasy Mini Kit (Qiagen, Valencia, CA) as suggested by the manufacturer. RNAs were then quantified and inspected by Bioanalyzer (Agilent Technologies) analysis.

tag: STAT3-/- MEF cell line


title: 12997942 - pBINT48 vs siT48

hyb_protocol: siT48 Cy5 / pBINT48 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: leaf - media : soil hygrometry : 70% temperature : 20°C Light : 12/12h

value: arabidopsis thaliana (columbia)  mutant (siplp2:silenced for expression of PLP2, a patatin-like LAH (At2g26560))


title: Chimpanzee liver, biological rep 3

value: liver, Gender:male, Age:30 years


title: STAT3-/- MEF cell line 02


title: STAT3+/+ MEF cell line 02

description: Spontaneously immortalized STAT3+/+ MEFs were grown in DMEM supplemented with 10% heat-inactivated FCS, 2 mM L-glutamine, 100 U/ml of penicillin, 100 μg/ml of streptomycin and maintained at 37°C in a 5% CO2 atmosphere. Cells were treated with Oncostatin M (OSM) (R&D Systems Inc.) at a final concentration of 20 ng/ml for 30 minutes.

source_name: cell line MEF

tag: STAT3+/+ MEF cell line


title: Chimpanzee cerebellum, biological rep 2

value: cerebellum, Gender:male, Age:37 years


title: 12997940 - pBINT48 vs seT48

hyb_protocol: seT48 Cy5 / pBINT48 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: STAT3-/- MEF cell line treated with OSM 03

tag: STAT3-/- MEF cell line treated with OSM


title: Chimpanzee cerebellum, biological rep 1

value: female

value: 27 years


title: Human cerebellum, pooled, technical rep 2

organism: Homo sapiens

source_name: human cerebellum

value: cerebellum (pooled from 24 donors)

value: male/female

value: 16-70 years


title: STAT3-/- MEF cell line treated with OSM 02


title: STAT3+/+ MEF cell line 03


title: Human cerebellum, pooled, technical rep 1


title: microdissected colorectal cancer CO973_2_1_1_1

status: Public on May 04 2009

city: Potsdam

first: Bernd

last: Hinzmann

address: Voltaireweg 4b

department: Molecular Profiling

country: Germany

institute: Signature Diagnostics AG

description: Gene expression data from microdissected CRC specimen

hyb_protocol: Hybridization of the labeled cRNA on the Affymetrix Chip were performed according to Affymetrix standard protocol.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings. Raw expression data was condensed to probe set-wise intensity values using the RMA algorithm.

molecule: polyA RNA

source_name: CRC patients undergoing elective standard oncological resection

label_protocol: For each sample, the cDNA synthesis and repetitive in vitro transcription were performed three times. The total amount of prepared mRNA from each sample was used. First strand cDNA synthesis was initiated using the Affymetrix T7-oligo-dT promoter-primer combination at 0.1 mM. The second strand cDNA synthesis was generated by internal priming. In vitro transcription was performed using the Megascript kit (Ambion, Huntington, UK) as recommended by Ambion. From the generated cRNA, a new first strand synthesis was initiated using 0.025 mM of a random hexamer as primer. After completion, the second strand synthesis was performed using the Affymetrix T7-oligo-dT promoter-primer combination. A second in vitro transcription was performed and then the procedure was repeated one additional time. During the last in vitro transcription, biotin-labeled ribonucleotides were incorporated into the aRNA, as recommended by the Affymetrix protocol.

extract_protocol:
All cancer specimens were snap frozen within 20 min following excision. After laser-capture microdissection frozen tissue specimens were serially cut into 6–8-μm-thick sections which were mounted on a sterile 2.5 mm membrane. Slides were fixed in 70% ethanol. The sections were briefly stained with haematoxylin and eosin, dehydrated in ethanol and dried for 10–15 min using an exsiccator. The membrane was turned around and fixed with adhesive tape on the other sterile slide. First slides served as a template on which the areas of tumor or normal epithelium were marked. On the consecutive section, these areas were microdissected using a laser microdissection system (SL, Jena, Germany and P.A.L.M. Microlaser Technologies AG Bernried, Germany) and capture transfer films (Arcturus GmbH, Moerfelden-Walldorf, Germany). For molecular analysis, up to 100,000 cells or approximately 30–60 mm2 of tissue section areas were pooled and collected in ice-cooled tubes containing 100 ml of 98% guanidine thiocyanate (GTC) buffer and 2% beta-mercaptoethanol.
PolyA mRNA from the microdissected specimens was prepared using the PolyA-tract 1000 kit (Promega, Heidelberg, Germany) according to the manufacturer’s recommendations.

tag: TumorLocalization

value: rectum lower third

tag: LymphNodesRemoved

tag: LymphNodesInvaded

tag: Death

tag: Rezidiv

tag: Gender

tag: AgeAtDiagnosis

tag: Grading

tag: pT

tag: pN

tag: pM

tag: UICC

value: I

tag: RectumOrColon

value: Rectum


title: STAT3+/+ MEF cell line tretated with OSM 02


title: microdissected colorectal cancer CO997_2_1_1_1

value: sigma

value: II

value: Colon


title: microdissected colorectal cancer CO913_2_1_1_1


title: Chimpanzee cerebellum, biological rep 1

tag: tissue

value: cerebellum, Gender:female, Age:27 years


title: microdissected colorectal cancer CO822_2_1_1_1

value: colon transversum


title: microdissected colorectal cancer CO7IT_2_1_1_1


title: microdissected colorectal cancer CO745_2_1_1_2

value: caecum

value: IV


title: microdissected colorectal cancer CO868_2_1_1_1

value: III


title: microdissected colorectal cancer CO704_2_1_1_1

value: rectum


title: microdissected colorectal cancer CO763_2_1_1_2


title: microdissected colorectal cancer CO797_2_1_1_1

value: colon ascending


title: microdissected colorectal cancer CO667_2_1_1_1


title: microdissected colorectal cancer CO636_2_1_1_2


title: microdissected colorectal cancer CO674_2_1_1_1

value: rectum middle third


title: microdissected colorectal cancer CO777_2_1_1_1


title: microdissected colorectal cancer CO557_2_1_1_1


title: microdissected colorectal cancer CO623_2_1_1_1


title: microdissected colorectal cancer CO741_2_1_1_2


title: microdissected colorectal cancer CO536_2_1_1_1


title: microdissected colorectal cancer CO528_2_1_1_1

value: rectum middle to lower third


title: microdissected colorectal cancer CO584_2_1_1_1


title: microdissected colorectal cancer CO510_2_1_1_1

value: rectum upper third


title: microdissected colorectal cancer CO6IT_2_1_1_2


title: microdissected colorectal cancer CO795_2_1_1_1


title: microdissected colorectal cancer CO590_2_1_1_1


title: NHGRI Ink4a-cht4 mv31952 (20071214)

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

description: Ink4a-cht4 vs Universal reference

hyb_protocol: The combined Cy3 and Cy5 labeled cDNAs are put in a total volume of 250 ul DEPC H20 and 250 ul of 2X Agilent hybridization buffer. The mixture is then denatured for 2 minutes and applied on the Agillent hybridization chamber/gasket slide in sandwich with the array slide. The hybridization is performed at 65 degre for 16 hours.

scan_protocol: Agilent Scanner

data_processing: IPLab/DeArray software, lowess normalization

label_protocol: 10-15 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Aminoallyl dUTP, after NaOH RNA hydrolysis, the labeled Aminoallyl dUTP cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104). The Aminoallyl dUTP cDNAs are then coupled with either Cy3 or Cy5 mono NHS Ester Dyes. The CyDyes labeled cDNAs are then purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104).

extract_protocol: RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns

tag: C57BL/6 melan Ink4a-cht4 melanocyte line

source_name: Stratagene Universal Mouse Reference RNA

extract_protocol: not applicable

tag: StratageneÕs Universal Mouse Reference RNA is a high-quality control for mouse-based microarray experiments that has quickly become an industry standard for mouse microarray experiments (see citation database). Comprised as a collection of RNA pooled from eleven cell lines


title: microdissected colorectal cancer CO533_2_1_1_1


title: NHGRI Ink4a-cht4 mv31951 (20071214)

description: Ink4a-cht4 vs Universal reference


title: NHGRI Ink4a-cht5 mv31946 (20071214)

description: Ink4a-cht5 vs Universal reference

tag: C57BL/6 melan Ink4a-cht5 melanocyte line


title: microdissected colorectal cancer CO501_2_1_1_1

tag: TumorLocalization

value: colon flexure right


title: NHGRI Ink4a-cht5 mv31950 (20071214)

description: Ink4a-cht5 vs Universal reference


title: microdissected colorectal cancer CO885_2_1_1_1

value: colon descending-sigm.

tag: LymphNodesRemoved


title: NHGRI Ink4a-b/b mv31944 (20071214)

description: Ink4a-b/b vs Universal reference

tag: C57BL/6 melan Ink4a-b melanocyte line


title: NHGRI Ink4a-cht5 mv31945 (20071214)

description: Ink4a-cht5 vs Universal reference


title: microdissected colorectal cancer CO427_2_1_1_1

value: rectum lower third

tag: LymphNodesInvaded

tag: Death


title: microdissected colorectal cancer CO438_2_1_1_1

tag: Rezidiv

tag: Gender

value: Rectum


title: microdissected colorectal cancer CO460_2_1_1_1

tag: AgeAtDiagnosis

tag: Grading


title: microdissected colorectal cancer CO425_2_1_1_1

tag: pT

tag: pN


title: NHGRI Ink4a-a/a mv31940 (20071214)

description: Ink4a-a/a vs Universal reference

tag: C57BL/6 melan Ink4a-1 melanocyte line


title: microdissected colorectal cancer CO418_2_1_1_2

value: rectum middle to upper third

tag: pM

tag: UICC

tag: RectumOrColon


title: NHGRI Ink4a-b/b mv31942 (20071214)

description: Ink4a-b/b vs Universal reference

tag: StratageneÕs Universal Mouse Reference RNA is a high-quality control for mouse-based microarray experiments that has quickly become an industry standard for mouse microarray experiments (see citation database). Comprised as a collection of RNA pooled from eleven cell lines


title: NHGRI Ink4a-a/a mv31941 (20071214)

description: Ink4a-a/a vs Universal reference


title: microdissected colorectal cancer CO482_2_1_1_1

value: sigma


title: microdissected colorectal cancer CO424_2_1_1_1

value: colon descending

value: II

value: Colon


title: NHGRI Ink4a-b/b mv31943 (20071214)

description: Ink4a-b/b vs Universal reference


title: NHGRI NIH3T3 mv31921 (20071214)

description: NIH3T3  vs Universal reference

tag: Mouse Swiss NIH embryo fibroblast


title: NHGRI NIH3T3 mv31923 (20071214)

description: NIH3T3  vs Universal reference


title: NHGRI NIH3T3 mv31922 (20071214)

description: NIH3T3  vs Universal reference


title: microdissected colorectal cancer CO20IT_2_1_1_1

tag: TumorLocalization


title: microdissected colorectal cancer CO15IT_2_1_1_1

tag: LymphNodesRemoved


title: microdissected colorectal cancer CO13IT_2_1_1_2


title: microdissected colorectal cancer CO22IT_2_1_1_1

value: x


title: microdissected colorectal cancer CO1144_2_1_1_1

value: I


title: microdissected colorectal cancer CO17IT_2_1_1_1

value: III


title: microdissected colorectal cancer CO29IT_2_1_1_1


title: microdissected colorectal cancer CO1137_2_1_1_1

value: rectum rektosigmoidaler transition


title: microdissected colorectal cancer CO18IT_2_1_1_2


title: microdissected colorectal cancer CO1133_2_1_1_1


title: microdissected colorectal cancer CO1117_2_1_1_1


title: microdissected colorectal cancer CO1116_2_1_1_1

value: rectum transition upper to middle third


title: microdissected colorectal cancer CO1130_2_1_1_1


title: microdissected colorectal cancer CO1058_2_1_1_1


title: microdissected colorectal cancer CO1048_2_1_1_2


title: microdissected colorectal cancer CO1073_2_1_1_1

value: rectum middle third


title: microdissected colorectal cancer CO1063_2_1_1_1


title: microdissected colorectal cancer CO1087_2_1_1_1


title: microdissected colorectal cancer CO1040_2_1_1_1


title: microdissected colorectal cancer CO1038_2_1_1_1


title: microdissected colorectal cancer CO1050_2_1_1_1


title: microdissected colorectal cancer CO1036_2_1_1_1

value: colon ascending


title: microdissected colorectal cancer CO1034_2_1_1_1


title: microdissected colorectal cancer CO480_2_1_1_1


title: ago3t2/ago3t3 (replicated 1)

status: Public on May 03 2009

city: Boston

first: Hualin

last: Xi

state: MA

address: 44 Cummington Street

institute: Boston University

description: Processed data: The first column is the transposon ids from flybase or transcript ids from RefSeq. The second column is the the summarized/normalized expression value.

hyb_protocol: Recommended Affymetrix protocol

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G according to manufacturer's instructions.

data_processing: Since transposons account for more than 10% of the probes on the tiling array, a special normalization workflow has been taken to avoid over-normalization of signals.  Coordinates and raw signal values for Drosophila tiling 2.0R array probes were extracted from Affymetrix Tiling Array Software.   Then probes mapped to transposon regions were identified. The remaining non-transposon probes were quantile-normalized across wild type and mutant replicates based on the assumption that the overall signal distribution of these probes should remain the same across the different strains. Then the signals for transposon probes were calculated by looking up the normalized values of non-transposon probes at same raw signal level. To summarize the signal for each transposon element, probes mapped to any copy of the element were grouped together and Hodges-Lehmann estimator (ref1) was used to calculate the pseudomedian of their normalized signals. We used pseudomedian as it is less sensitive to the large number of outlier probes (probes with value of 1) in the tiling array experiments. Differentially expressed transposon elements were identified by contrasting their pseudomeidan values in three mutant replicates against three wild type replicates. To correct for multiple testing, False Discovery Rates (FDRs) were calculated from t-test P-values.  FDR<0.02 were used to call significantly changed transposons. Transposons with average expression value less than a minimal expression threshold of 149 (the 50th percentile expression value of RefSeq mRNAs) in both wild type and mutants were flagged as they are at the detection limit of the tiling array. Expression values of mRNAs were summarized by calculating the pseudomedian of probes mapped to each of the RefSeq mRNA transcripts. Differentially expressed transcripts were identified using FDR<0.02 cutoff.

label: Biotin

organism: Drosophila melanogaster

source_name: ago3t2/ago3t3 (replicated 1)

label_protocol: GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix)

growth_protocol: Adult 2-4 day old female flies were fed yeast paste and maintained at 25˚C.

extract_protocol: The RNA was purified using Qiagen RNAeasy® kit following the manufacturer's protocol (Qiagen)

tag: Total RNA purified from whole ovaries from 2-4 day old flies.


title: ago3t2/ago3t3 (replicated 3)

source_name: ago3t2/ago3t3 (replicated 3)


title: P[ry +t7.2=PZ]rhi02096 cn/P{SUP or-P}KG00910 (replicated 2)


title: P[ry +t7.2=PZ]rhi02096 cn/P{SUP or-P}KG00910 (replicated 1)


title: microdissected colorectal cancer CO1025_2_1_1_1

value: rectum

tag: LymphNodesInvaded


title: ago3t2/ago3t3 (replicated 2)

source_name: ago3t2/ago3t3 (replicated 2)


title: microdissected colorectal cancer CO1030_2_1_1_1

tag: Death


title: aubHN2 cn bw/ aubQC42 cn bw (replicated 3)

source_name: aubHN2 cn bw/ aubQC42 cn bw (replicated 1)


title: P[ry +t7.2=PZ]rhi02096 cn/P{SUP or-P}KG00910 (replicated 3)


title: microdissected colorectal cancer CO1028_2_1_1_1

value: colon

tag: Rezidiv


title: microdissected colorectal cancer CO1018_2_1_1_1

tag: Gender


title: P[W+]armi1/armi72.1 RNA (replicated 1)

source_name: P[W+]armi1/armi72.1 RNA (replicated 1)


title: P[W+]armi1/armi72.1 RNA (replicated 2)

source_name: P[W+]armi1/armi72.1 RNA (replicated 2)


title: P[W+]armi1/armi72.1 RNA (replicated 3)

source_name: P[W+]armi1/armi72.1 RNA (replicated 3)


title: NHGRI Ink4a-cht4 mv31953 (20071214)

description: Ink4a-cht4 vs Universal reference

tag: C57BL/6 melan Ink4a-cht4 melanocyte line


title: aubHN2 cn bw/ aubQC42 cn bw (replicated 1)


title: W1118 RNA (replicated 3)

source_name: W1118 RNA (replicated 3)


title: W1118 RNA (replicated 1)

source_name: W1118 RNA (replicated 1)


title: W1118 RNA (replicated 2)

source_name: W1118 RNA (replicated 2)


title: aubHN2 cn bw/ aubQC42 cn bw (replicated 2)


title: OKT-3/IL-2 16h 2

status: Public on May 02 2009

city: Munich

first: Guenther

middle: HS

last: Richter

address: Parzivalstr. 16

department: Pediatrics & Children's Cancer Research Center

institute: Klinikum rechts der Isar, TU-Muenchen

description:
cultured PBMC, IL-2 treated
PBMC were stimulated for 16 hrs with 100 ng/ml OKT-3 together with 100 U/ml recombinant human interleukin-2

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Microarray Suite 5.0 was used with the data and for normalization by scaling all probe sets to 500.

label: biotin, streptavidin-phycoerytrin

source_name: PBMC

label_protocol: A total of 10 µg RNA from each sample was used to prepare biotinylated target cRNA as previously described (Staege MS, Hutter C, Neumann I, et al. DNA microarrays reveal relationship of Ewing family tumors to both endothelial and fetal neural crest-derived cells and define novel targets. Cancer Res 2004;64:8213-21). A detailed protocol is available at www.affymetrix.com.

growth_protocol: Cells were cultivated in RPMI 1640 medium containing 10 % FCS with additional 1 % penicillin/streptomycin in a humidified atmosphere at 37 °C and 5 % CO2

extract_protocol: Total RNA was prepared with acid phenol/chloroform extraction (TRIzol, Invitrogen; Karlsruhe, Germany) followed by purification with RNeasy Mini Kit (Qiagen; Hilden, Germany) according to the manufacturer’s instructions and was quantified spectro-photometrically. The quality of the purified RNA was assessed by agarose gel analysis.

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from human peripheral blood samples (obtained with IRB approval and informed consent) by centrifugation over Ficoll-Paque (GE Healthcare, Freiburg, Germany). Isolated PBMCs were cultured at 106 cells in RPMI 1640 supplemented with 10 % FCS (both Biochrom, Berlin, Germany) and antibiotics and incubated at different time points with 100 ng/ml OKT-3 and 100 U/ml IL-2 ± 30 µg/ml anti-CD25 antibody

tag: cell type

value: PBMC


title: OKT-3/IL-2 16h, anti-CD25 1

description:
cultured PBMC, IL-2 and anti-CD25 treated
PBMC were stimulated for 16 hrs with 100 ng/ml OKT-3 together with 100 U/ml recombinant human interleukin-2 presence of 30 µg/ml anti-CD25 antibody.


title: OKT-3/IL-2 8h, anti-CD25 1

description:
cultured PBMC, IL-2 and anti-CD25 treated
PBMC were stimulated for 8 hrs with 100 ng/ml OKT-3 together with 100 U/ml recombinant human interleukin-2 presence of 30 µg/ml anti-CD25 antibody.


title: OKT-3/IL-2 8h 2

description:
cultured PBMC, IL-2 treated
PBMC were stimulated for 8 hrs with 100 ng/ml OKT-3 together with 100 U/ml recombinant human interleukin-2


title: MouseMG_MMTV-CRE;SOX9F/F_REP4

city: Worcester

first: Shaolei

last: Lu

address: 364 Plantation Street

department: Cancer Biology

institute: University of Massachusetts Medical School

description: UMASS MED GENOMICS CORE PROTOCOL

hyb_protocol: UMASS MED GENOMICS CORE PROTOCOL

scan_protocol: UMASS MED GENOMICS CORE PROTOCOL

data_processing: PLIER EXPRESSION CONSOLE 1.0

label: UMASS MED GENOMICS CORE PROTOCOL

source_name: MouseMG_MMTV-CRE;SOX9F/F T26L

label_protocol: UMASS MED GENOMICS CORE PROTOCOL

growth_protocol: ROUTINE MAINTENANCE

extract_protocol: QIAGEN RNEASY MINI KIT

treatment_protocol: VIRGIN MICE, NO TREATMENT

tag: strain

value: C57BL/6 X FVB

tag: gender

value: FEMALE

tag: age

value: 5 WKS

tag: tissue

value: MAMMARY GLAND

tag: genotype

tag: tissue id


title: OKT-3/IL-2 16h, anti-CD25 2


title: OKT-3/IL-2 16h 1


title: OKT-3/IL-2 8h 1


title: MouseMG_MMTV-CRE;SOX9+/F_REP3

description: UMASS MED GENOMICS CORE PROTOCOL

source_name: MouseMG_MMTV-CRE;SOX9+/F R38


title: No treatment 3

description:
cultured PBMC, nontreated
untreated PBMC


title: MouseMG_MMTV-CRE;SOX9F/F_REP3

description: UMASS MED GENOMICS CORE PROTOCOL

source_name: MouseMG_MMTV-CRE;SOX9F/F S96


title: No treatment 2


title: OKT-3/IL-2 8h, anti-CD25 2


title: No treatment 1


title: MouseMG_MMTV-CRE;SOX9F/F_REP2

description: UMASS MED GENOMICS CORE PROTOCOL

source_name: MouseMG_MMTV-CRE;SOX9F/F S31


title: MouseMG_MMTV-CRE;SOX9F/F_REP1

description: UMASS MED GENOMICS CORE PROTOCOL

source_name: MouseMG_MMTV-CRE;SOX9F/F S06


title: 13288441_rep7_Cy3_EM

city: Manhattan

first: Joseph

last: Coolon

state: KS

address: 264 Chalmers Hall

department: Biology

institute: Kansas State University

description: This is one channel of a duel channel array where we did not use ratios and instead used each channel separately and therefore we have uploaded the channels separately.

hyb_protocol: Hybridization was performed on a Tecan HS400 Hybridization Station (Tecan Inc., Zurich, Switzerland) at the Kansas State University Gene Expression Facility.  Hybridization protocol is as follows: 1) place microarrays in hybridization station and clamp shut. 2) Prehybridization: Wash with prehybridization solution – Wash 30sec, Soak 30sec @ 55º C 3) Wash 15 sec Prehybridization solution soak 0sec @ 55º C 4) Probe injection: inject probe (120µl) @ 42º C 5) Hybridization: @42º C for 16 hours with medium agitation frequency 6) Washes: Wash with wash solution 1 for 1 min and soak 3 min @ 42º C 7) Wash with wash solution 2 for 1 min and soak 3 min @ 23º C 8) Wash with wash solution 3 for 1 min and soak 3 min @ 23º C 9) Wash with wash solution 3 for 30 sec@ 23º C 10) Probe injection: inject dendromers @ 23º C 11) Hybridization: @23º C for 3 hours with medium agitation frequency 12) Washes: Wash with wash solution 1 for 1 min and soak 3 min @ 42º C 13) Wash with wash solution 2 for 1 min and soak 3 min @ 23º C 14) Wash with wash solution 3 for 1 min and soak 3 min @ 23º C 15) Slide drying: @ 30º C air dry slide for 2 min. Prehybridization solution: 2X SSC, 0.2% SDS, + BSA Wash solution 1: 2X SSC, 0.2% SDS Wash solution 2: 2X SSC Wash solution 3: 0.2X SSC

scan_protocol: Hybridized arrays were scanned with an Axon GenePix 4000B (MDS Analytical Technologies, Toronto, Canada) and data was collected using GenePix 5.1 software (MDS Analytical Technologies).

data_processing: Background subtracted intensity values were used for input into statistical analysis.

organism: Caenorhabditis elegans

source_name: whole animal, Adults aged 1 week, E. coli environment

label_protocol:
Indirect labeling was used with the Genisphere Array 350 kit according to manufacturers recommendations for the hybridization station.
CDNA synthesis:
1. In a microtube, prepare the RNA-RT primer mix:
1-10µl total RNA (1-5µg mammalian total RNA or 2.5-10µg plant total RNA)
1µl RT primer (Vial 2, 1pmole/µl, either Cy3/Alexa Fluor 546 or Cy5/Alexa Fluor 647)
Add Nuclease Free Water (Vial 10) to a final volume of 11µl
2. Mix the RNA-RT primer mix and microfuge briefly to collect contents in the bottom of the tube.
3. Heat to 80°C for 10 minutes and immediately transfer to ice for 2-3 minutes.
4. In a separate microtube on ice, prepare a reaction mix for every RT reaction:
4 µl 5X SuperScript II First Strand Buffer (or equivalent reaction buffer supplied with enzyme)
2 µl 0.1M dithiothreitol (if supplied with enzyme; otherwise use Nuclease Free Water (Vial 10))
1 µl dNTP mix (Vial 3)
1 µl Superase-In™ RNase inhibitor (Vial 4)
1 µl Superscript II enzyme, 200 units (or equivalent reverse transcriptase)
5. Gently mix (do not vortex) the reaction mix and microfuge briefly to collect reaction mix contents in the bottom of
the tube. Keep on ice until used.
6. Add the 9µl of reaction mix from step 5 to the 11µl of RNA-RT primer mix from step 3 (20µl volume).
7. Gently mix (do not vortex) and incubate at 42°C for 2 hours.
8. Stop the reaction by adding 3.5µl of 0.5M NaOH/50mM EDTA.
9. Incubate at 65°C for 15 minutes to denature the DNA/RNA hybrids and degrade the RNA.
10. Neutralize the reaction with 5µl of 1M Tris-HCl, pH 7.5.
3DNA preparation:
1. Prepare the 3DNA Array 350 Capture Reagent (Vial 1). It is necessary to break up aggregates that may form as a result of the freezing process.
a. Thaw the 3DNA Array 350 Capture Reagent (Vial 1) in the dark at room temperature for 20 minutes.
b. Vortex at the maximum setting for 3 seconds and microfuge briefly.
c. Incubate at 50-55°C for 10 minutes.
d. Vortex at the maximum setting for 3-5 seconds.
e. Microfuge the tube briefly to collect the contents at the bottom.
Be sure to check the sample for aggregates prior to use and repeat vortex mixing if necessary. Aggregates may appear as small air bubbles or flakes at the side of the tube below the surface of the solution. Repeat steps a-e if necessary.
2. Thaw and resuspend the 2X Hybridization Buffer (Vial 6 or Vial 7) by heating to 70°C for at least 10 minutes or until completely resuspended. Vortex to ensure that the components are resuspended evenly. If necessary, repeat heating and vortexing until all the material has been resuspended. Microfuge for 1 minute. Warning: Do not use the 2X Enhanced cDNA Hybridization Buffer (Vial 12) in the 3DNA Hybridization step.
3. For each array, prepare a 3DNA Hybridization Mix accordingly.
4. Gently vortex and briefly microfuge the 3DNA Hybridization Mix. Incubate the 3DNA Hybridization Mix first at 75-80°C for 10 minutes, and then at the hybridization temperature until loading the array (see the table located below step 7 for recommended hybridization temperatures). Pre-warm the microarrays to the hybridization temperature.
5.  Gently vortex and briefly microfuge the 3DNA Hybridization Mix. Add the 3DNA Hybridization Mix to microarray on step 10 of Hybridization protocol, taking care to leave behind any precipitate at the bottom of the tube.

growth_protocol: Bacteria was grown in liquid culture to stardard OD and spread on Nematode growth media agar plates (100mm).  Bacteria was allowed to grow 1 day until bacterial lawn was a constant thickness.  Adult nematodes were then bleached to decontaminate and isolate eggs.  Eggs were added to spread bacterial plates in a constant quantity.  Nematodes were allowed to grow for 7 days and washed from plates and sieved with a 400 mesh sieve to retain only adults.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to manufacturer recommendations.
1. Add 8 ml of TRIZOL to 2 ml packed worms in 15 ml centrifuge tube. Vortex and invert tube to solubilize and lyse worms for at least 10 min.
2. Divide into two 15 ml c/f tubes--5 ml each.
3. Invert for additional 5 min. Solution should be pink and will contain thread-like material. Spin at 4°C, 4000 rpm for 20 min to remove insoluble material. All spins done in fixed angle rotor with white inserts.
4. Transfer supernatant to new 15 ml c/f tubes(2). Add 800  l chloroform to each tube.
5. Vortex 15 sec, incubate at room temperature for 3 min. Smeary preps will result if vortexing not long enough.
6. Spin at 4°C, 4000 rpm for 20 min to separate phases.
7. Transfer upper phase to new 15 ml c/f tubes(2). Add 2 ml isopropanol to each tube.
8. Invert to mix & incubate at RT for 10 min. Spin at 4°C, 4000 rpm for 30 min.
9. Remove s/n with pipet without disturbing the pellet.
10. Add 400 ul 75% EtOH, vortex briefly.
11. Spin at 4°C, 4000 rpm for 10 min.
12. Remove s/n with pipet and invert racked tubes in hood with door half shut. Approx. 10-15 minutes; do not overdry.
13. Add 300  l DEPC-treated ddH2O to each tube and resuspend and combine tubes using wide opening tips. May have to heat briefly at 45-50°C to completely dissolve. Really good yields may require adding more H2O.
Store at -80°C in 1 mg aliquots.

treatment_protocol: Growth on bacterial environment E. coli OP50

value: Wildtype Bristol (N2)

tag: sex

value: Hermaphrodite

value: 7 days

value: whole animal

tag: bacterial environment

value: E. coli OP50

tag: growth media

value: nematode growth media


title: MouseMG_MMTV-CRE;SOX9+/F_REP4

description: UMASS MED GENOMICS CORE PROTOCOL

source_name: MouseMG_MMTV-CRE;SOX9+/F R39


title: 13288442_rep7_Cy5_PB

source_name: whole animal, Adults aged 1 week, Bacillus megaterium environment

treatment_protocol: Growth on bacterial environment Bacillus megaterium

value: Bacillus megaterium


title: MouseMG_MMTV-CRE;SOX9+/F_REP2

description: UMASS MED GENOMICS CORE PROTOCOL

source_name: MouseMG_MMTV-CRE;SOX9+/F R37


title: 13288442_rep7_Cy3_PB

source_name: whole animal, Adults aged 1 week, Pseudomonas sp. environment

treatment_protocol: Growth on bacterial environment Pseudomonas sp.

value: Pseudomonas sp.


title: 13288440_rep7_Cy3_MP

source_name: whole animal, Adults aged 1 week, Micrococcus luteus environment

treatment_protocol: Growth on bacterial environment Micrococcus luteus

value: Micrococcus luteus


title: No treatment 4


title: 13288440_rep7_Cy5_MP


title: 13288439_rep7_Cy5_EB


title: 13288437_rep6_Cy5_BP


title: 13288438_rep7_Cy5_PE


title: 13288438_rep7_Cy3_PE


title: 13288441_rep7_Cy5_EM


title: 13288439_rep7_Cy3_EB


title: 13228205_rep7_Cy3_BM


title: 13288436_rep6_Cy5_ME


title: 13228209_rep5_Cy5_BP


title: 13288436_rep6_Cy3_ME


title: 13228204_rep6_Cy3_BE


title: 13228206_rep6_Cy5_MB


title: 13288437_rep6_Cy3_BP


title: 13228205_rep7_Cy5_BM


title: 13201482_rep5_Cy3_BM


title: 13201482_rep5_Cy5_BM


title: 13228204_rep6_Cy5_BE


title: 13228209_rep5_Cy3_BP


title: 13228202_rep6_Cy5_EP


title: 13288434_rep6_Cy3_PM


title: 13228206_rep6_Cy3_MB


title: 13201481_rep5_Cy3_EB


title: 13288434_rep6_Cy5_PM


title: 13228202_rep6_Cy3_EP


title: 13201481_rep5_Cy5_EB


title: 13201479_rep5-Cy5_MP


title: 13201478_rep5_Cy3_PE


title: 13201476_rep4_Cy5_EM


title: 13201477_rep5_Cy5_ME


title: 13228201_rep4_Cy5_EP


title: 13201478_rep5_Cy5_PE


title: 13201475_rep4_Cy3_PB


title: 13201479_rep5_Cy3_MP


title: 13228201_rep4_Cy3_EP


title: 13201477_rep5_Cy3_ME


title: 13201476_rep4_Cy3_EM


title: 13201474_rep4_Cy5_PM


title: 13201475_rep4_Cy5_PB


title: 13201460_rep3_Cy5_MB


title: 13228208_rep3_Cy5_PE


title: 13228208_rep3_Cy3_PE


title: 13201460_rep4_Cy3_MB

source_name: whole animal, Adults aged 1 week, Micrococcus Luteus environment


title: 13201473_rep4_Cy5_BE


title: 13201473_rep4_Cy3_BE

source_name: whole animal, Adults aged 1 week, Bacillus megateriumenvironment


title: 13201466_rep3_Cy3_BP


title: 13228207_rep3_Cy3_BM


title: 13228207_rep3_Cy5_BM


title: 13201474_rep4_Cy3_PM


title: 13201463_rep3_Cy5_MP


title: 13201463_rep3_Cy3_MP


title: 13201466_rep3_Cy5_BP


title: Hyb9: OD00001_HCP3_N2_MXEMB_3

status: Public on May 01 2009

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description:
channel ch1 is control channel;
channel ch2 is ChIP channel; lab: Desai; reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55; short description: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen; catalog: Desai Lab; company: Other; clonal: Polyclonal; purified: Affinity; antigen: N-terminal histone tail of HCP-3; host: Rabbit; species: C. elegans; target name: HCP-3; aliases: CeCENP-A; official name: OD00001_HCP3;

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User's Guide.

data_processing: ChIP-chip_normalization_standard_nimblegen_v1. The log2-ratio ratio of intensity from sample/reference channel was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. This was performed using NimbleScan software according to the NimbleScan v2.4 User's Guide and chapter 6 of the NimbleGen Arrays User's Guide ChIP-chip Analysis (version 3.1, 27 May 2008) at Roche NimbleGen. Genome version is WS180.

label: Cy3 dye

molecule: genomic DNA

growth_protocol: Worm_embryo_growth_and_harvest_vRG1. Synchronized worm cultures were grown at 20 C in batches of 500 ml using 2.8-L Fernbach flasks shaking at 230 rpm. Gravid adults were separated from debris by sucrose floating. Embryos were isolated by bleaching and fixed after chitinase treatment with 1 % formaldehyde for 10 min on ice. For a detailed protocol see http://www.modencode.org/.

extract_protocol:
Worm_embryo_extraction_vRG1. Fixed embryos were suspended in 5 volumes of ChIP buffer (50 mM Hepes-KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) and sonicated on ice with a Branson sonifier microtip (30 % power setting for 3 min; 40 % power setting for 1 min).  Debris were pelleted at 10 000 g for 20 min and the supernatant was made 10 % in glycerol.  The extract was snap frozen in liquid nitrogen aliquots containing 3 mg of protein and stored at -80 C.
Worm_chromatin_immunoprecipitation_vRG1. For each ChIP reaction, 3 mg of protein extract was diluted with ChIP buffer (50 mM Hepes KOH pH 7.6, 140 NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5 % NP-40) to 900 ul.  Then 35 ul 30 % sarcosyl (1 % final) and 20 ul 5 % Na-deoxycholate (0.1 % final) were added.  50 ul of the diluted extract were removed (input sample), mixed with Elution buffer (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 250 mM NaCl, 1 % SDS) and processed as described for ChIP samples.  100 ul antibody/bead suspension (5ug antibody pre-bound to 50 ul Dynabeads, suspended in ChIP buffer) was added and the mixture and rotated over night at 4 C.  Beads were washed 2 times; 1 ml FA Buffer (50 mM Hepes-KOH pH 7.6, 150 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 5 min each; with 1 ml FA-1000 buffer (50 mM Hepes-KOH pH 7.6, 1 M NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml FA-500 buffer (50 mM Hepes-KOH pH 7.6, 500 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 0.1 % Na-deoxycholate) for 10 min; with 1 ml TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% NP-40, 1% Na-deoxycholate) for 10 min; and briefly with 1 ml TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA).  Immunocomplexes were eluted with 50 ul Elution buffer for 15 min at 67 C.  Eluates were incubated over night at 65 C to reverse cross-links, then treated with proteinase K (0.44 mg/ml) at 37 C for 2 h.  Nucleic acids were recovered by phenol/chloroform extraction and ethanol precipitation.  After digestion with RNAse A (0.33 mg/ml) for 2h at 37 C, DNA was purified using the Qiagen PCR purification kit.
Worm_LM-PCR_Amplification_for_ChIP-chip_vRG1. ChIP and input DNA was blunt ended with T4 polymerase for 20 min at 12 C and purified by phenol/chloroform extraction and EtOH precipitation. Annealed oligonucleotide linkers (oligo 1: gcggtgacccgggagatctgaattc; oligo 2: gaattcagatc) were ligated to the DNA fragments over night at 16 C. The ligated DNA was precipitated with EtOH, disolved in 10 mM Tris-HCl pH 8, and amplified with a Taq/Pfu polymerase mix using oligo 1. For a detailed protocol see http://www.modencode.org/.

tag: developmental stage

value: embryo

label: Cy5 dye

tag: lab

value: Desai

tag: reference

value: Monen et al. (2005) Nat Cell Biol 7:1248-55

tag: catalog

value: Desai Lab

tag: company

value: Other

tag: clonal

value: Polyclonal

tag: purified

value: Affinity

tag: antigen

value: N-terminal histone tail of HCP-3

tag: host

value: Rabbit

tag: species

value: C. elegans

tag: target name

tag: aliases

value: CeCENP-A

tag: official name


title: 1319585_rep3_Cy5_ME

tag: strain

value: Wildtype Bristol (N2)

value: Hermaphrodite

tag: age

value: 7 days

tag: tissue

value: whole animal


title: Hyb4: OD00001_HCP3_N2_MXEMB_2

label_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User's Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42C.

value: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen


title: Hyb3: OD00001_HCP3_N2_MXEMB_1

tag: genotype

value: wild type

value: DR subclone of DB original (Tc1 pattern I)

tag: source


title: Hyb7: OD00001_HCP3_N2_MXEMB_3

description:
channel ch1 is ChIP channel; lab: Desai; reference: Monen et al. (2005) Nat Cell Biol 7: 1248-55; short description: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen; catalog: Desai Lab; company: Other; clonal: Polyclonal; purified: Affinity; antigen: N-terminal histone tail of HCP-3; host: Rabbit; species: C. elegans; target name: HCP-3; aliases: CeCENP-A; official name: OD00001_HCP3;
channel ch2 is control channel;

tag: developmental stage

value: embryo

tag: lab

value: Desai


title: Hyb8: OD00001_HCP3_N2_MXEMB_3

tag: reference

value: Monen et al. (2005) Nat Cell Biol 7:1248-55

tag: catalog

value: Desai Lab


title: Hyb1: OD00001_HCP3_N2_MXEMB_1

tag: company

value: Other

tag: clonal

value: Polyclonal


title: 13228212_rep2_Cy3_BE

tag: sex

tag: bacterial environment

value: Bacillus megaterium

tag: growth media

value: nematode growth media


title: Hyb5: OD00001_HCP3_N2_MXEMB_2

tag: purified

value: Affinity

tag: antigen

value: N-terminal histone tail of HCP-3

tag: host

value: Rabbit

tag: species

value: C. elegans

tag: target name


title: Hyb2: OD00001_HCP3_N2_MXEMB_1

tag: strain

tag: official name

tag: aliases

value: CeCENP-A


title: 13228210_rep2_Cy3_EM

value: Wildtype Bristol (N2)

value: Hermaphrodite

tag: age

value: 7 days

tag: tissue

value: whole animal

value: E. coli OP50


title: 13228212_rep2_Cy5_BE


title: 112_rep2_Cy5_MB


title: Hyb6: OD00001_HCP3_N2_MXEMB_2

tag: developmental stage

value: embryo

tag: lab

value: Desai

tag: reference

value: A GST fusion of the HCP-3 N-terminal histone tail was injected into rabbit and the serum affinity-purified against a 6His fusion of the antigen


title: 105_rep2_Cy5_PM

value: Micrococcus luteus


title: 111_rep2_Cy5_PB


title: 111_rep2_Cy3_PB

value: Pseudomonas sp.


title: 1319585_rep3_Cy3_ME

source_name: whole animal, Adults aged 1 week, Micrococcus luteusenvironment


title: 13228210_rep2_Cy5_EM


title: 112_rep2_Cy3_MB


title: 105_rep2_Cy3_PM


title: 13198581_rep3_Cy3_EB


title: Oncocytoma kidney tumor sample, biological rep12

status: Public on Apr 28 2009

first: Hasan

middle: Huseyin

last: Otu

address: 4 Blackfan Circle Rm. 238

department: Medicine

institute: Harvard Medical School

description: Affymetrix HG-U133A gene expression data from Oncocytoma kidney tumor sample.

hyb_protocol: Following fragmentation, ~5 microg of cRNA were hybridized for 16 hr at 45C on Human Genome 133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing:
The data in the Sample table were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM)-mismatch (MM) difference model. In the dChip analysis, array outliers are not treated as missing expression values and no truncation on signal values is applied.

Signal values from a MAS5 analysis are available in the 'GSE15641_mas5_data.txt' file, which is linked to the GSE15641 record as as supplementary file.

source_name: cancerous human kidney tissue, oncocytoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Kidney


title: Oncocytoma kidney tumor sample, biological rep11


title: Oncocytoma kidney tumor sample, biological rep10


title: 114_rep2_Cy5_EP

value: nematode growth media


title: Oncocytoma kidney tumor sample, biological rep8


title: Oncocytoma kidney tumor sample, biological rep3


title: Oncocytoma kidney tumor sample, biological rep9


title: Oncocytoma kidney tumor sample, biological rep5


title: Oncocytoma kidney tumor sample, biological rep4


title: Oncocytoma kidney tumor sample, biological rep2


title: Oncocytoma kidney tumor sample, biological rep6


title: 114_rep2_Cy3_EP


title: 13198581_rep3_Cy5_EB

value: Bacillus megaterium


title: Oncocytoma kidney tumor sample, biological rep1


title: chromophobe RCC kidney tumor sample, biological rep1

description: Affymetrix HG-U133A gene expression data from chromophobe RCC kidney tumor sample.

source_name: cancerous human kidney tissue, chromophobe RCC


title: chromophobe RCC kidney tumor sample, biological rep5


title: Transitional cell cancer kidney tumor sample, biological rep6

description: Affymetrix HG-U133A gene expression data from Transitional Cell Carcinoma kidney tumor sample.

source_name: cancerous human kidney tissue, transitional cell carcinoma


title: chromophobe RCC kidney tumor sample, biological rep6


title: Oncocytoma kidney tumor sample, biological rep7


title: Transitional cell cancer kidney tumor sample, biological rep7


title: Transitional cell cancer kidney tumor sample, biological rep8


title: Transitional cell cancer kidney tumor sample, biological rep5


title: chromophobe RCC kidney tumor sample, biological rep3


title: chromophobe RCC kidney tumor sample, biological rep4


title: Transitional cell cancer kidney tumor sample, biological rep4


title: chromophobe RCC kidney tumor sample, biological rep2


title: Transitional cell cancer kidney tumor sample, biological rep1


title: papillary RCC kidney tumor sample, biological rep11

description: Affymetrix HG-U133A gene expression data from papillary RCC kidney tumor sample.

source_name: cancerous human kidney tissue, papillary RCC


title: papillary RCC kidney tumor sample, biological rep9


title: papillary RCC kidney tumor sample, biological rep10


title: Transitional cell cancer kidney tumor sample, biological rep2


title: papillary RCC kidney tumor sample, biological rep4


title: Transitional cell cancer kidney tumor sample, biological rep3


title: papillary RCC kidney tumor sample, biological rep5


title: papillary RCC kidney tumor sample, biological rep8


title: papillary RCC kidney tumor sample, biological rep1


title: papillary RCC kidney tumor sample, biological rep6


title: papillary RCC kidney tumor sample, biological rep2


title: papillary RCC kidney tumor sample, biological rep3


title: clear cell RCC kidney tumor sample, biological rep31

description: Affymetrix HG-U133A gene expression data from clear cell RCC kidney tumor sample.

source_name: cancerous human kidney tissue, clear cell RCC


title: papillary RCC kidney tumor sample, biological rep7


title: clear cell RCC kidney tumor sample, biological rep30


title: clear cell RCC kidney tumor sample, biological rep32


title: clear cell RCC kidney tumor sample, biological rep27


title: clear cell RCC kidney tumor sample, biological rep29


title: clear cell RCC kidney tumor sample, biological rep24


title: clear cell RCC kidney tumor sample, biological rep23


title: clear cell RCC kidney tumor sample, biological rep26


title: clear cell RCC kidney tumor sample, biological rep25


title: clear cell RCC kidney tumor sample, biological rep19


title: clear cell RCC kidney tumor sample, biological rep22


title: clear cell RCC kidney tumor sample, biological rep20


title: clear cell RCC kidney tumor sample, biological rep28


title: clear cell RCC kidney tumor sample, biological rep17


title: clear cell RCC kidney tumor sample, biological rep9


title: clear cell RCC kidney tumor sample, biological rep16


title: clear cell RCC kidney tumor sample, biological rep8


title: clear cell RCC kidney tumor sample, biological rep10


title: clear cell RCC kidney tumor sample, biological rep13


title: clear cell RCC kidney tumor sample, biological rep18


title: clear cell RCC kidney tumor sample, biological rep5


title: clear cell RCC kidney tumor sample, biological rep11


title: clear cell RCC kidney tumor sample, biological rep3


title: clear cell RCC kidney tumor sample, biological rep6


title: clear cell RCC kidney tumor sample, biological rep21


title: clear cell RCC kidney tumor sample, biological rep14


title: clear cell RCC kidney tumor sample, biological rep4


title: clear cell RCC kidney tumor sample, biological rep12


title: clear cell RCC kidney tumor sample, biological rep7


title: normal kidney sample, biological rep20

description: Affymetrix HG-U133A gene expression data from normal kidney sample.

source_name: normal human kidney tissue


title: normal kidney sample, biological rep17


title: normal kidney sample, biological rep22


title: clear cell RCC kidney tumor sample, biological rep2


title: clear cell RCC kidney tumor sample, biological rep15


title: normal kidney sample, biological rep21


title: normal kidney sample, biological rep23


title: normal kidney sample, biological rep18


title: normal kidney sample, biological rep19


title: normal kidney sample, biological rep16


title: normal kidney sample, biological rep15


title: normal kidney sample, biological rep9


title: normal kidney sample, biological rep2


title: normal kidney sample, biological rep8


title: normal kidney sample, biological rep4


title: normal kidney sample, biological rep5


title: normal kidney sample, biological rep12


title: normal kidney sample, biological rep1


title: normal kidney sample, biological rep10


title: normal kidney sample, biological rep3


title: normal kidney sample, biological rep11


title: normal kidney sample, biological rep13


title: normal kidney sample, biological rep6


title: normal kidney sample, biological rep14


title: L9 flowering Bio rep1_B Rep 1 RicechipB

status: Public on Apr 22 2009

city: Beijing

first: lihuang

last: Zhu

address: Datun Road, Chaoyang District,100101 Beijing China

department: Plant Gene Research Center

country: China

institute: The Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences (CAS)

description: One biological replication unit coming from pools of 3~6 individual samples

hyb_protocol: 42C 50% formamide

scan_protocol: Packard Scanarray Lite

data_processing: For each slide, spots flagged bad by Genepix were removed from the latter analysis step. Then based on the spot signals distribution of positive and negative controls among hybridization data, the threshold for expression was determined with false positive below 5%, only those genes expressed at least two independent replications were kept for further analysis. The filtered data set was normalized based on the median of all expressed genes to normalize the intensity of different experiments, and normalization of two channels of each array was done using intensity-based loess method with R language.

organism: Oryza sativa

source_name: 93-11,flowering, flag leaf

label_protocol: amino-allyl and monofunctional dye

extract_protocol: Guanidinium Isothiocyanate(Molecular cloning III)

value: flag leaf

tag: development stage

value: flowering

tag: environment

value: rice field

source_name: LYP9,flowering, flag leaf


title: L9 flowering Bio rep1_B Rep 4 RicechipB


title: LP flowering Bio rep1_B Rep 4 RicechipB

source_name: PA64s,flowering, flag leaf


title: normal kidney sample, biological rep7


title: LP filling panicle Bio rep1_B Rep 4 RicechipB

source_name: PA64s,filling, panicle

value: panicle

value: filling

source_name: LYP9,filling, panicle


title: LP flowering Bio rep1_B Rep 1 RicechipB


title: LP filling panicle Bio rep1_B Rep 3 RicechipB


title: LP flowering Bio rep1_B Rep 2 RicechipB


title: L9 flowering Bio rep1_B Rep 3 RicechipB


title: L9 flowering Bio rep1_B Rep 2 RicechipB


title: LP filling flag leaf Bio rep1_B Rep 2 RicechipB

source_name: LYP9,filling, flag leaf

source_name: PA64s,filling, flag leaf


title: LP filling flag leaf Bio rep1_B Rep 4 RicechipB


title: LP filling panicle Bio rep1_B Rep 2 RicechipB


title: LP flowering Bio rep1_B Rep 3 RicechipB


title: L9 filling flag leaf Bio rep1_B Rep 1 RicechipB

source_name: 93-11,filling, flag leaf


title: L9 filling panicle Bio rep1_B Rep 2 RicechipB

source_name: 93-11,filling, panicle


title: L9 filling panicle Bio rep1_B Rep 3 RicechipB


title: L9 filling flag leaf Bio rep1_B Rep 4 RicechipB


title: LP filling flag leaf Bio rep1_B Rep 1 RicechipB


title: L9 filling flag leaf Bio rep1_B Rep 3 RicechipB


title: L9 filling panicle Bio rep1_B Rep 1 RicechipB


title: L9 filling flag leaf Bio rep1_B Rep 2 RicechipB


title: LP filling flag leaf Bio rep1_B Rep 3 RicechipB


title: LP heading Bio rep1_B Rep 1 RicechipB

source_name: LYP9,heading, flag leaf

value: heading

source_name: PA64s,heading, flag leaf


title: LP filling panicle Bio rep1_B Rep 1 RicechipB


title: L9 heading Bio rep1_B Rep 2 RicechipB

source_name: 93-11,heading, flag leaf


title: L9 filling panicle Bio rep1_B Rep 4 RicechipB


title: LP heading Bio rep1_B Rep 2 RicechipB


title: LP booting Bio rep1_B Rep 3 RicechipB

source_name: LYP9,booting, flag leaf

value: booting

source_name: PA64s,booting, flag leaf


title: L9 booting Bio rep1_B Rep 1 RicechipB

source_name: 93-11,booting, flag leaf


title: LP booting Bio rep1_B Rep 2 RicechipB


title: L9 heading Bio rep1_B Rep 3 RicechipB


title: LP seedling Bio rep1_B Rep 3 RicechipB

source_name: LYP9,seedling, shoot

value: the green part

value: 7 days old

value: culture room

source_name: PA64s,seedling, shoot


title: L9 Tilling Bio rep1_B Rep 1 RicechipB

source_name: LYP9,tilling, shoot

value: leaf

value: tilling

source_name: 93-11,tilling, shoot


title: LP seedling Bio rep1_B Rep 1 RicechipB


title: LP Tilling Bio rep1_B Rep 3 RicechipB

source_name: PA64s,tilling, shoot


title: L9 booting Bio rep1_B Rep 4 RicechipB

source_name: 93-11,booting, leaf

source_name: LYP9,booting, leaf


title: L9 heading Bio rep1_B Rep 4 RicechipB


title: LP heading Bio rep1_B Rep 3 RicechipB


title: L9 seedling Bio rep1_B Rep 1 RicechipB

source_name: 93-11,seedling, shoot


title: LP booting Bio rep1_B Rep 4 RicechipB


title: LP Tilling Bio rep1_B Rep 2 RicechipB


title: L9 booting Bio rep1_B Rep 2 RicechipB


title: L9 seedling Bio rep1_B Rep 2 RicechipB


title: L9 Tilling Bio rep1_B Rep 3 RicechipB


title: L9 Tilling Bio rep1_B Rep 2 RicechipB


title: LP seedling Bio rep1_B Rep 2 RicechipB


title: L9 flowering Bio rep1_A Rep 1 RicechipA

source_name: LYP9,flowering, flag leaf

source_name: 93-11,flowering, flag leaf


title: LP flowering Bio rep1_A Rep 1 RicechipA

source_name: PA64s,flowering, flag leaf


title: LP filling panicle Bio rep1_A Rep 1 RicechipA

source_name: PA64s,filling, panicle

source_name: LYP9,filling, panicle


title: LP filling flag leaf Bio rep1_A Rep 3 RicechipA

source_name: LYP9,filling, flag leaf

source_name: PA64s,filling, flag leaf


title: L9 filling panicle Bio rep1_A Rep 4 RicechipA

source_name: 93-11,filling, panicle


title: L9 filling panicle Bio rep1_A Rep 3 RicechipA


title: L9 flowering Bio rep1_A Rep 2 RicechipA


title: LP filling flag leaf Bio rep1_A Rep 1 RicechipA


title: LP filling panicle Bio rep1_A Rep 3 RicechipA


title: LP filling flag leaf Bio rep1_A Rep 4 RicechipA


title: L9 filling panicle Bio rep1_A Rep 2 RicechipA


title: L9 filling flag leaf Bio rep1_A Rep 2 RicechipA

source_name: 93-11,filling, flag leaf


title: L9 filling flag leaf Bio rep1_A Rep 3 RicechipA


title: LP flowering Bio rep1_A Rep 2 RicechipA


title: L9 filling flag leaf Bio rep1_A Rep 4 RicechipA


title: LP flowering Bio rep1_A Rep 3 RicechipA


title: LP filling panicle Bio rep1_A Rep 2 RicechipA


title: L9 filling flag leaf Bio rep1_A Rep 1 RicechipA


title: LP filling panicle Bio rep1_A Rep 4 RicechipA


title: LP filling flag leaf Bio rep1_A Rep 2 RicechipA


title: L9 flowering Bio rep1_A Rep 4 RicechipA


title: LP heading Bio rep1_A Rep 3 RicechipA

source_name: LYP9,heading, flag leaf

source_name: PA64s,heading, flag leaf


title: LP heading Bio rep1_A Rep 2 RicechipA


title: LP booting Bio rep1_A Rep 5 RicechipA

source_name: LYP9,booting, flag leaf

source_name: PA64s,booting, flag leaf


title: LP booting Bio rep1_A Rep 1 RicechipA


title: L9 heading Bio rep1_A Rep 3 RicechipA

source_name: 93-11,heading, flag leaf


title: L9 heading Bio rep1_A Rep 1 RicechipA


title: LP booting Bio rep1_A Rep 2 RicechipA


title: LP heading Bio rep1_A Rep 1 RicechipA


title: L9 seedling Bio rep1_B Rep 3 RicechipB

source_name: LYP9,seedling, shoot


title: L9 heading Bio rep1_A Rep 2 RicechipA


title: L9 Tilling Bio rep1_A Rep 1 RicechipA

source_name: LYP9,tilling, shoot

source_name: 93-11,tilling, shoot


title: L9 booting Bio rep1_A Rep 3 RicechipA

source_name: 93-11,booting, flag leaf


title: LP Tilling Bio rep1_A Rep 1 RicechipA

source_name: PA64s,tilling, shoot


title: LP Tilling Bio rep1_A Rep 3 RicechipA


title: L9 Tilling Bio rep1_A Rep 3 RicechipA


title: L9 filling panicle Bio rep1_A Rep 1 RicechipA


title: L9 booting Bio rep1_A Rep 2 RicechipA


title: LP flowering Bio rep1_A Rep 4 RicechipA

source_name: LYP9,flowering, flag leaf

source_name: PA64s,flowering, flag leaf


title: LP seedling Bio rep1_A Rep 2 RicechipA

source_name: PA64s,seedling, shoot


title: LP seedling Bio rep1_A Rep 3 RicechipA


title: LP Tilling Bio rep1_A Rep 2 RicechipA


title: L9 seedling Bio rep1_A Rep 3 RicechipA

source_name: 93-11,seedling, shoot


title: L9 seedling Bio rep1_A Rep 2 RicechipA


title: L9 seedling Bio rep1_A Rep 1 RicechipA


title: L9 flowering Bio rep1_A Rep 3 RicechipA

source_name: 93-11,flowering, flag leaf


title: Breast_tumor2_rep2

status: Public on Apr 13 2009

city: Sao Paulo

first: Barbara

middle: Pereira

last: Mello

state: SP

address: R. Prof. Antonio Prudente, 211

department: Centro de Pesquisa

country: Brazil

institute: Hospital A. C. Camargo

description: Reference RNA: Daudi (Burkitt's lymphoma), DLD-1 (colorectal adenocarcinoma), DU 145 (prostate carcinoma), FaDu (pharinx squamous cell carcinoma), GM-637 (fibroblast), H-146 (small cell lung carcinoma), HT-1080 (fibrosarcoma), HB4a (normal mammary luminal epithelium), HEK (human embryonic kidney), Jurkat (acute T cell leukemia), Saos-2 (osteosarcoma), SK-BR-3 (breast adenocarcinoma), SK-MEL-28 (melanoma), T24 (bladder transitional cell carcinoma), T98G (glioblastoma multiforme).

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 2 ug Cot1 DNA; 5X Denhardts ; 10 ug Salmon sperm, Deionized formamide 40%  / Temperature:42 / Time:12-24h / Touch Down: 70, 55, 50, 42 Washing - Round 1 - Solution: 2X SSC 0,1% SDS / Temperature:42 / Time:4 min / Washing Number: 1 Washing - Round 2 - Solution: 0,1 SSC 0,1% SSC / Temperature:42 / Time:4 min / Washing Number: 1 Washing - Round 3 - Solution: 0,1X SSC / Temperature:42 / Time:rinse / Washing Number: 3 Washing - Round 4 - Solution: 0,1X SSC / Temperature:42 / Time:4 min / Washing Number: 4 Washing - Round 5 - Solution: 0,1X SSC / Temperature:42 / Time:rinse / Washing Number: 5

scan_protocol: Slides were scanned on a confocal laser scanner (ScannArray Express, Perkin Elmer), using identical parameters for all slides and data was extracted with ScanArray Express software (Perkin Elmer). Glass Slides were scanned at different photomultiplier tube (pmt) gains, being 70% and 60% for the channels 1 (Alexa Fluor 555) and 2 (Alexa Fluor 647), respectively.

data_processing: After subtracting local background, data was normalized by Lowess (R Project) and dye swaps were reversed during normalization.

label: Alexa 555

source_name: reference RNA pool

label_protocol: Alexa 555 label protocol

extract_protocol: Trizol

tag: RNA pool of 15 distinct cell lines

label: Alexa 647

source_name: breast cancer

label_protocol: Alexa 647 label protocol

tag: infiltrating duct breast carcinoma


title: Bone_marrow_tumor2_rep2

description: Reference RNA: Daudi (Burkitt's lymphoma), DLD-1 (colorectal adenocarcinoma), DU 145 (prostate carcinoma), FaDu (pharinx squamous cell carcinoma), GM-637 (fibroblast), H-146 (small cell lung carcinoma), HT-1080 (fibrosarcoma), HB4a (normal mammary luminal epithelium), HEK (human embryonic kidney), Jurkat (acute T cell leukemia), Saos-2 (osteosarcoma), SK-BR-3 (breast adenocarcinoma), SK-MEL-28 (melanoma), T24 (bladder transitional cell carcinoma), T98G (glioblastoma multiforme)

source_name: bone marrow cancer

tag: acute myeloid leukemia


title: Breast_tumor3_rep1


title: Breast_tumor3_rep2


title: Bone_marrow_tumor3_rep1

tag: acute lymphoblastic leukemia


title: Bone_marrow_tumor2_rep1


title: Bone_marrow_tumor3_rep2


title: Bone_marrow_normal3_rep2

source_name: normal bone marrow tissue

tag: normal bone marrow tissue


title: Bone_marrow_normal3_rep1


title: Bone_marrow_tumor1_rep1


title: L9 booting Bio rep1_A Rep 5 RicechipA

source_name: LYP9,booting, flag leaf


title: Bone_marrow_tumor1_rep2


title: L9 Tilling Bio rep1_A Rep 2 RicechipA


title: Esophagus_normal4_rep2

source_name: normal esophagus tissue

tag: normal esophagus tissue


title: Breast_tumor2_rep1


title: Bone_marrow_normal2_rep2


title: Esophagus_normal4_rep1


title: Bone_marrow_normal2_rep1


title: Bone_marrow_normal1_rep1


title: Esophagus_normal3_rep1


title: Esophagus_normal2_rep2


title: Esophagus_normal3_rep2


title: Esophagus_normal2_rep1


title: Breast_normal3_rep2

source_name: normal breast tissue

tag: normal breast tissue


title: Breast_normal3_rep1


title: Uterus_normal1_rep2

source_name: normal uterus tissue

tag: normal uterus tissue


title: Uterus_normal3_rep1


title: Breast_normal2_rep1


title: Breast_normal1_rep1


title: Uterus_normal1_rep1


title: Breast_normal1_rep2


title: Uterus_normal2_rep1


title: Placenta_normal4_rep1

source_name: normal placenta tissue

tag: normal placenta tissue


title: Uterus_normal3_rep2


title: Uterus_normal2_rep2


title: Placenta_normal3_rep2


title: Uterus_tumor3_rep2

source_name: uterus cancer

tag: uterus adenocarcinoma


title: Head_neck_tumor3_rep1

source_name: head & neck cancer

tag: epidermoid head & neck carcinoma - tongue


title: Head_neck_tumor3_rep2


title: Placenta_normal2_rep1


title: Breast_normal2_rep2


title: Placenta_normal4_rep2


title: Placenta_normal2_rep2


title: Testis_normal3_rep1

source_name: normal testis tissue

tag: normal testis tissue


title: Testis_normal3_rep2


title: Uterus_tumor3_rep1


title: Placenta_normal3_rep1


title: Head_neck_tumor2_rep2


title: Head_neck_tumor2_rep1


title: Thyroid_normal3_rep2

source_name: normal thyroid tissue

tag: normal thyroid tissue - goiter


title: LP Tilling Bio rep1_B Rep 1 RicechipB

source_name: LYP9,tilling, shoot

tag: strain

tag: tissue

source_name: PA64s,tilling, shoot


title: Placenta_normal1_rep2


title: Head_neck_tumor1_rep2

tag: epidermoid head & neck carcinoma - neck


title: Thyroid_normal3_rep1


title: Testis_normal2_rep1


title: Head_neck_tumor1_rep1


title: Placenta_normal1_rep1


title: Head_neck_normal1_rep2

source_name: normal head & neck tissue

tag: ormal head & neck tissue - palate_maxilla


title: Lung_normal1_rep1

source_name: normal lung tissue

tag: nnormal lung tissue

tag: RNA pool of 15 distinct cell lines


title: Lung_normal1_rep2

source_name: reference RNA pool

tag: normal lung tissue


title: Breast_tumor1_rep2

source_name: breast cancer

tag: infiltrating duct breast carcinoma


title: Uterus_tumor2_rep2


title: Uterus_tumor2_rep1


title: Head_neck_normal1_rep1

tag: normal head & neck tissue - palate_maxilla


title: Testis_normal2_rep2


title: Breast_tumor1_rep1


title: Uterus_tumor1_rep2


title: Colon_tumor2_rep2

source_name: colon cancer

tag: colon adenocarcinoma


title: Colon_tumor2_rep1


title: Uterus_tumor1_rep1


title: Colon_tumor1_rep2


title: Colon_normal1_rep1

source_name: normal colon tissue

tag: normal colon tissue


title: Colon_normal1_rep2


title: Colon_tumor1_rep1


title: Prostate_tumor3_rep2

source_name: prostate cancer

tag: prostate adenocarcinoma


title: Prostate_normal3_rep2

source_name: normal prostate tissue

tag: normal prostate tissue


title: Prostate_normal3_rep1


title: Prostate_tumor3_rep1


title: Prostate_normal2_rep2


title: Esophagus_tumor1_rep2

source_name: esophagus cancer

tag: esophagus adenocarcinoma


title: Prostate_tumor2_rep1


title: Esophagus_tumor2_rep1

tag: squamous cell esophagus carcinoma


title: Stomach_normal3_rep2

source_name: normal stomach tissue

tag: normal stomach tissue


title: Esophagus_tumor1_rep1


title: Stomach_tumor2_rep2

source_name: stomach cancer

tag: stomach adenocarcinoma


title: Prostate_normal2_rep1


title: Esophagus_normal1_rep2

source_name: normal esophagus tissue

tag: normal esophagus tissue


title: Stomach_normal1_rep2


title: Stomach_normal3_rep1


title: Esophagus_normal1_rep1


title: Stomach_normal2_rep1


title: Stomach_normal2_rep2


title: Stomach_tumor1_rep1

tag: gastrointestinal stromal stomach carcinoma


title: Stomach_tumor1_rep2


title: Stomach_normal1_rep1


title: Prostate_tumor2_rep2


title: Prostate_tumor1_rep2


title: Thyroid_normal2_rep2

tag: normal thyroid tissue


title: Prostate_tumor1_rep1


title: Thyroid_normal2_rep1


title: Thyroid_tumor3_rep2

source_name: thyroid cancer

tag: papillary/follicular thyroid carcinoma


title: Thyroid_tumor3_rep1


title: Thyroid_tumor2_rep2


title: Testis_normal1_rep1

source_name: normal testis tissue

tag: normal testis tissue


title: Testis_normal1_rep2

tag: RNA pool of 15 distinct cell lines


title: Prostate_normal1_rep1


title: Thyroid_tumor2_rep1


title: Thyroid_tumor1_rep2


title: Thyroid_tumor1_rep1


title: Prostate_normal1_rep2


title: Thyroid_normal1_rep2

source_name: normal thyroid tissue


title: Thyroid_normal1_rep1


title: Esophagus_tumor2_rep2


title: Stomach_tumor2_rep1


title: Bone_marrow_normal1_rep2

source_name: normal bone marrow tissue

tag: normal bone marrow tissue


title: D-allose_rep2

status: Public on Apr 02 2009

city: Miki

first: Kazuya

last: Akimitsu

state: Kagawa

address: 2393, Ikenobe

department: Faculty of Agriculture

country: Japan

institute: Kagawa University

description: An Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA) was used for the microarray analysis. By using RNeasy plant mini kit (Qiagen, Hilden, Germany), total RNA was extracted from shoots of two-leaf stage rice plants that had been treated with 0.5 mM D-allose, 0.5 mM D-glucose, or no sugar for 2 days. For each biological replicate, material from at least five rice plants was pooled to provide a single sample for RNA extraction. We performed 3 biological replicates for each treatment. All microarray procedures and data analyses were performed according to the manufacturer’s instructions. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Redwood City, CA, USA). Total RNA (400 ng) was labeled with Cy-3 or Cy-5 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). Fluorescently labeled targets were hybridized to Agilent Rice Oligo Microarrays for 17 h at 65°C. After hybridization, following wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray Scanner (G2505B and software G2565BA; Agilent Technologies).

hyb_protocol: Kit: in situ hybridization kit plus Manufacturer: Agilent Technologies

scan_protocol: Scan protocol Scanner: Agilent DNA microarray scanner Manufacturer: Agilent Technologies

data_processing: Feature extraction software (version 9.1; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer’s instructions.

source_name: Rice shoots, treated with 0.5 mM D-allose.

label_protocol:
Kit: Low input RNA linear amplification kit
Manufacturer: Agilent Technologies

extract_protocol:
Kit: RNeasy plant mini kit
Manufacturer: Qiagen

treatment_protocol: Rice plants are treated with 0.5 mM D-allose for 2 days.

tag: cultivar

value: a Japonica cultivar "Nipponbare"

tag: leaf-stage

tag: tissue

value: shoot

source_name: Rice shoots, mock-treated.

treatment_protocol: Rice plants are mock-treated for 2 days.


title: D-allose_rep1


title: D-glucose_rep3

source_name: Rice shoots, treated with 0.5 mM D-glucose.


title: CEBPAsilencedAML_#1

status: Public on Jan 21 2009

city: Rotterdam

first: Bas

last: Wouters

address: P.O. Box 2040, room Ee1330B

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA, log2 transformation

source_name: AML blasts, CEBPA silenced

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was extracted by lysis with guanidium isothiocyanate followed by cesium chloride gradient purification.

tag: Male, 21 years, CEBPA silenced, FAB M1, Normal cytogenetics


title: small airways, smoker 041

status: Public on Dec 19 2008

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: Comparison of gene expression in airway epithelial cells of normal non-smokers, phenotypic normal smokers, smokers with early COPD, and smokers with COPD.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: age

tag: sex

value: M

tag: ethnic group

value: white

tag: smoking status

value: smoker, 20 pack-years


title: D-allose_rep3


title: small airways, non-smoker 014

value: non-smoker


title: small airways, non-smoker 019

value: F


title: small airways, smoker 048

value: black

value: smoker, 37 pack-years


title: small airways, non-smoker 006


title: D-glucose_rep2


title: D-glucose_rep1


title: small airways, non-smoker 008


title: PKGI KO vs. WT brown adipose tissues replicate 1

status: Public on Dec 31 2008

city: Bonn

first: Peter

last: Mayer

address: Kurt-Georg-Kiesinger-Allee

institute: Fed. Inst. for Drugs and Med. Devices

description: all stepa according to the manufacturer's (Agilent) recommendations

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: DNA microarray scanner (Agilent)

data_processing: Agilent Feature Extraction Software default lowess normalization

label: Cy3 (green)

source_name: WT

label_protocol: Agilent Low RNA Input Linear Amp Kit

treatment_protocol: untreated

value: brown adipose

tag: genotype

value: WT

tag: genetic background

label: Cy5 (red)

source_name: PKGI KO

value: PKGI KO


title: C9: hr 96 dox (-)

status: Public on Sep 28 2008

city: South San Francisco

first: Robert

last: Stull

state: CA

address: 384 Oyster Point Blvd, Suite #8

department: Genomics

institute: VistaGen Therapeutics

description: ***** These records currently present results containing only probes for the Wnt, BMP/TFGb, and Notch pathways as published in Chen et al., 2008, Nature Biotechnology.  The full set of processed and raw data tables will be available by June 1, 2009. *****

scan_protocol: see CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection, using Axon 4000B scanner

data_processing: median normalization, CodeLink Expression Analysis, filtered for Wnt, BMP/TFGb, and Notch pathway probesets

source_name: Ainv18 mouse ES cells engineered to overexpress activated Notch4 upon doxycycline treatment

label_protocol: see CodeLink Gene Expression System: Manual Labelled cRNA target Preparation

growth_protocol: ES cells were maintained on irradiated feeders in Dulbecco€'s Modified Eagle Medium (DMEM) supplemented with 15% fetal calf serum (FCS), 10% ES cell conditioned medium, penicillin, streptomycin, 1.5 x 10^-4 M monothioglycerol (MTG; Sigma) and LIF (1% conditioned medium).  Prior to induction of differentiation, cells were passaged 2 times on gelatin-coated plates in Iscove Modified Dulbecco Medium (IMDM) containing the same supplements mentioned above to deplete the population of feeder cells.  ).  Prior to induction of differentiation, cells were passaged 2 times on gelatin-coated plates in Iscove Modified Dulbecco Medium (IMDM) containing the same supplements mentioned above to deplete the population of feeder cells.  For the generation of EBs, the cells were harvested and cultured in 60 mm low attachment Petri grade dishes (VWR) with IMDM supplemented with 2 mM L-glutamine (Gibco/BRL), 200 Âµg/mL transferrin (Boehringer Mannheim), 0.5 mM ascorbic acid (Sigma), 4 x 10^-4 M MTG plus 15% FCS.

extract_protocol: Qiagen RNeasy Mini protocol for isolation of total RNA from animal cells, with on column Dnase treatment.

treatment_protocol: For reaggregation cultures to support the differentiation of the hematopoietic and vascular lineages, 3 x 10^5 Flk-1+ cells/ml (harvested at d3.5 after addition of serum) were cultured for 24 hours in ultra-low attachment 24-well plates (Corning Costar) with the EB differentiation medium (above) plus 5% Protein-Free Hybridoma Medium-II (PFHM-II, Invitrogen), either in the presence or absence of dox.  After 24 hours, the cells were washed and cultured without doxycycline for up to an additional 3 days.  Total RNA was harvested from dox-treated or dox-null cultures at 4, 12, 24, 48, or 96 hours.

tag: biological replicate 3

tag: hour = 96


title: C7: hr 48 dox (-)

hyb_protocol: see CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection

tag: hour = 48


title: C6: hr 24 dox (+)

tag: hour = 24

tag: doxycycline treatment


title: C8: hr 48 dox (+)


title: PKGI KO vs. WT brown adipocytes replicate 1

treatment_protocol: Adipocytes were differentiated in vitro from brown adipose tissue

tag: cell type

value: brown adipocytes


title: C10: hr 96 dox (+)


title: C4: hr 12 dox (+)

tag: hour = 12


title: C5: hr 24 dox (-)


title: B8: hr 48 dox (+)

tag: biological replicate 2


title: C2: hr 4 dox (+)

tag: hour = 4


title: B9: hr 96 dox (-)


title: B10: hr 96 dox (+)


title: small airways, non-smoker 003


title: B5: hr 24 dox (-)


title: B3: hr 12 dox (-)


title: B7: hr 48 dox (-)


title: A7: hr 48 dox (-)

tag: biological replicate 1


title: B4: hr 12 dox (+)


title: B6: hr 24 dox (+)


title: A10: hr 96 dox (+)


title: A6: hr 24 dox (+)


title: A4: hr 12 dox (+)


title: A8: hr 48 dox (+)


title: A3: hr 12 dox (-)


title: B2: hr 4 dox (+)


title: A5: hr 24 dox (-)


title: A9: hr 96 dox (-)


title: B1: hr 4 dox (-)


title: C3: hr 12 dox (-)


title: A2: hr 4 dox (+)


title: Rheumatoid arthritis, synovial membrane patient EB30 (U133A)

status: Public on Sep 02 2008

city: Hannover

first: René

last: Huber

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Institute for Clinical Chemistry

institute: Hannover Medical School

description: see publication for details

hyb_protocol: according to supplier´s instructions, Affymetrix

scan_protocol: by laser scanning (Hewlett Packard gene scanner)

data_processing: background corrected signal intensities were determined using the MAS 5.0 software (Affymetrix)

source_name: synovial membrane patient EB30 (rheumatoid arthritis)

extract_protocol: according RNeasy Kit, Qiagen

treatment_protocol:
NSARD,
prednisolone,
MTX

value: f

tag: disease

value: rheumatoid arthritis


title: C1: hr 4 dox (-)


title: GSY504-CBS1484

status: Public on Jul 23 2008

city: Stanford

last: Dunn

department: Genetics

institute: Stanford University

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70569.gif
Strain Name: GSY504=CBS1484

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Barbara,,Dunn

data_processing: VALUE is log10(test/reference)

organism: Saccharomyces cerevisiae

source_name: Scer 350ng + Sbay 350ng sonicated genomic DNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: GSY504 genomic DNA, 350 ng, HaeIII cut

tag: strain name


title: Rheumatoid arthritis, synovial membrane patient EB30 (U133B)

description: see publication for details

label_protocol: according to supplier´s instructions, Affymetrix

tag: sex

tag: age


title: A1: hr 4 dox (-)


title: GSY133

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70568.gif
Strain Name: Strain name aliases: GSY133=CBS1486=DBVPG6258=NCYC397

value: Scer 350ng + Sbay 350ng sonicated genomic DNA

source_name: GSY133 genomic DNA, 350 ng, HaeIII cut


title: GSY516

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70729.gif
Strain Name: GSY516=CBS6903

source_name: Sbay CBS7001 + Scer S288C  genomic DNA sonicated, 350 ng ea

source_name: GSY516 genomic DNA 350 ng HaeIII cut


title: Self-HaeIII-Sbay-Scer

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70573.gif
Strain Name: control

source_name: Scer 400ng + Sbay 300ng sonicated genomic DNA

source_name: Sbay Zymo prep 300 ng, HaeIII cut, Scer Zymo prep 100 ng, HaeIII cut plus 300ng uncut

value: control


title: GSY129-22Aug06-65Wash

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70308.gif
Strain Name: GSY129=CBS1513=DBVPG6033

source_name: Scer + Sbay genomic each DNA 350 ng sonicated

source_name: GSY129 genomic DNA 350 ng HaeIII cut


title: GSY134-22Aug06-65Wash

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70307.gif
Strain Name: GSY134=CBS1503=DBVPG6261

value: Scer + Sbay genomic each DNA 350 ng sonicated

source_name: GSY134 genomic DNA 350 ng HaeIII cut


title: GSY138

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70567.gif
Strain Name: GSY138=DBVPG6285

source_name: GSY138 genomic DNA, 350 ng, HaeIII cut


title: GSY137

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70572.gif
Strain Name: GSY137=DBVPG6284

source_name: GSY137 genomic DNA, 350 ng, HaeIII cut


title: GSY136-22Aug06-65Wash

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70309.gif
Strain Name: GSY136=DBVPG6283

source_name: GSY136 genomic DNA 350 ng HaeIII cut


title: GSY509

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70720.gif
Strain Name: GSY509=CBS2440=NCYC398

value: Sbay CBS7001 + Scer S288C  genomic DNA sonicated, 350 ng ea

source_name: GSY509 genomic DNA 350 ng HaeIII cut


title: GSY508-CBS2156

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70565.gif
Strain Name: GSY508=CBS2156=CBS457

value: Scer 400ng + Sbay 300ng sonicated genomic DNA

source_name: GSY508 genomic DNA, 350 ng, HaeIII cut


title: GSY503-CBS1483

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70570.gif
Strain Name: GSY503=CBS1483

source_name: Scer  350ng + Sbay 350ng sonicated genomic DNA

source_name: GSY503 genomic DNA, 350 ng, HaeIII cut


title: GSY135

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70306.gif
Strain Name: GSY135=DBVPG6283

source_name: Scer + Sbay genomic DNA 350 ng each sonicated

source_name: GSY135 genomic DNA 350 ng HaeIII cut


title: GSY501-CBS1174

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70564.gif
Strain Name: GSY501=CBS1174

source_name: GSY501 genomic DNA, 350 ng, HaeIII cut


title: GSY139-22Aug06-65Wash

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70310.gif
Strain Name: GSY139=DBVPG6560

source_name: GSY139 genomic DNA 350 ng HaeIII cut


title: Sbay + Scer HaeIII 65Wash

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70304.gif
Strain Name: control

value: Scer + Sbay genomic DNA 350 ng each sonicated

source_name: Sbay + Scer genomic DNA 350 ng HaeIII cut


title: GSY132

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70571.gif
Strain Name: GSY132=CBS1260=DBVPG6257=NCYC400

source_name: Scer 350ng + Sbay 350ng sonicated genomic DNA

source_name: GSY132 genomic DNA, 350 ng, HaeIII cut


title: GSY131

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70566.gif
Strain Name: GSY131=CBS1538=DBVPG6047=NCYC392

source_name: GSY131 genomic DNA, 350 ng, HaeIII cut


title: Self-HaeIII vs Self-Sonicated

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70302.gif
Strain Name: control

source_name: Sbay + Scer genomic DNA 350 ng each sonicated

source_name: Sbay + Scer genomic DNA  350 ng each HaeIII cut


title: small airways, non-smoker 002

description: Comparison of gene expression in airway epithelial cells of normal non-smokers, phenotypic normal smokers, smokers with early COPD, and smokers with COPD.

source_name: airway epithelial cells obtained by bronchoscopy and brushing

value: M

tag: ethnic group

value: white

tag: smoking status


title: GSY515

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70721.gif
Strain Name: GSY515=CBS5832

source_name: Sbay CBS7001 + Scer S288C  genomic DNA sonicated, 350 ng ea

source_name: GSY515 genomic DNA 350 ng HaeIII cut


title: Expression data of colon cancer 426B

status: Public on Aug 26 2005

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

institute: Jichi Medical University

description: Characteristics definitions: Well=well-differentiated adenocarcinoma; Mod=moderately differentiated adenocarcinoma; Sig=signet ring cell adenocarcinoma; Muc=mucinous adenocarcinoma. Methylation of AXIN2 promoter region was determined by COBRA method.

source_name: Patient ID426-B

extract_protocol: mRNA was amplified from the specimens and was used to prepare biotin-labeled cRNA for hybridization.

tag: patient id

tag: age (years)

value: Female

tag: msi status

value: Negative

tag: mlh1 methylation

value: No

tag: braf gene

value: Wild

tag: kras2 gene

tag: tumor site

value: Proximal

tag: dukes stage

value: C

tag: pathology

value: Well

tag: axin2 methylation


title: Expression data of colon cancer 419B

source_name: Patient ID419-B

value: Mutant

value: D

value: Muc


title: Expression data of colon cancer 249B

source_name: Patient ID249-B

value: Male

value: B


title: Expression data of colon cancer 308B

source_name: Patient ID308-B

value: Distal

value: Mod


title: Expression data of colon cancer 295B

source_name: Patient ID295-B


title: Expression data of colon cancer 307B

source_name: Patient ID307-B


title: Expression data of colon cancer 238B

source_name: Patient ID238-B

value: A


title: Expression data of colon cancer 298B

source_name: Patient ID298-B


title: Expression data of colon cancer 319B

source_name: Patient ID319-B


title: Expression data of colon cancer 278B

source_name: Patient ID278-B


title: Expression data of colon cancer 433B

source_name: Patient ID433-B

value: Positive

value: Yes


title: Expression data of colon cancer 416B

source_name: Patient ID416-B

value: Female


title: Expression data of colon cancer 413B

source_name: Patient ID413-B


title: Expression data of colon cancer 336B

source_name: Patient ID336-B


title: Expression data of colon cancer 479B

source_name: Patient ID479-B


title: Expression data of colon cancer 280B

source_name: Patient ID280-B


title: Expression data of colon cancer 263B

source_name: Patient ID263-B


title: Expression data of colon cancer 225B

source_name: Patient ID225-B


title: Expression data of colon cancer 305B

source_name: Patient ID305-B

value: Sig


title: Expression data of colon cancer 318B

source_name: Patient ID318-B


title: Expression data of colon cancer 308A

source_name: Patient ID308-A

value: Negative

value: No


title: Expression data of colon cancer 298A

source_name: Patient ID298-A

value: Wild

value: Proximal


title: Expression data of colon cancer 278A

source_name: Patient ID278-A

value: C

value: Well


title: Expression data of colon cancer 426A

source_name: Patient ID426-A


title: Expression data of colon cancer 307A

source_name: Patient ID307-A


title: Expression data of colon cancer 419A

source_name: Patient ID419-A

value: Mutant

value: D


title: Expression data of colon cancer 319A

source_name: Patient ID319-A


title: Expression data of colon cancer 238A

source_name: Patient ID238-A

value: Male


title: Expression data of colon cancer 249A

source_name: Patient ID249-A

value: B


title: Expression data of colon cancer 416A

source_name: Patient ID416-A

value: Muc


title: Expression data of colon cancer 479A

source_name: Patient ID479-A

value: Mod


title: Expression data of colon cancer 433A

source_name: Patient ID433-A


title: Expression data of colon cancer 295A

source_name: Patient ID295-A


title: Expression data of colon cancer 305A

source_name: Patient ID305-A


title: Expression data of colon cancer 318A

source_name: Patient ID318-A


title: Expression data of colon cancer 280A

source_name: Patient ID280-A


title: Expression data of colon cancer 413A

source_name: Patient ID413-A

value: A


title: Expression data of colon cancer 225A

source_name: Patient ID225-A

value: Positive


title: Expression data of colon cancer 263A

source_name: Patient ID263-A

value: Yes


title: Expression data of colon cancer 336A

source_name: Patient ID336-A


title: Mo17Ch1greenUV2

status: Public on Sep 01 2004

city: Wilmington

first: Ann

last: Stapleton

state: NC

address: 601 S. College

department: Biological Sciences

institute: University of North Carolina Wilmington

description:
Inbred lines B73 and Mo17, from the same stocks used to create the IBM mapping lines, were kindly supplied by M. Lee.  These lines were increased in the field nursery at Clayton, NC. Individual seeds were placed one per 6 cm pot filled with vermiculite, at a density of 36 pots per flat, and grown in the greenhouse without supplemental lighting for ten days to the two-leaf stage.  The greenhouse photosynthetically active radiation levels are ~20% less than outdoor radiation.  The two lines were then exposed to 4 h of ultraviolet radiation from UV313 bulbs (Q Panel, Westlake, OH, USA) suspended about 30 cm above the plants.  The UV dose was measured at plant height using the UV-B sensor on an International Light radiometer Model IL1400A (International Light, Newburyport, MA); the treatment plants received a total UV dose of 86 Jm-2.  Control plants were placed under UV313 bulbs that were covered with polyester (MylarD, US Plastics, Lima, OH, USA), which transmits visible light but excludes UV-B.  After UV irradiation the UV bulbs were turned off and the plants were allowed to recover for 4 h in the greenhouse.  The second and third seedling leaf from each of four plants was harvested and dropped immediately into liquid nitrogen.  Pooling assured sufficient RNA and also decreases biological variability.  Total RNA was extracted from frozen tissue using Trizol (Invitrogen Co., Carlsbad, CA), as described in the microarray manufacturer’s protocol (http://www.zmdb.iastate.edu/zmdb/microarray/protocols.html#P3).  PolyA-plus messenger RNA was prepared from the total RNA using a Qiagen Oligotex kit (Qiagen Corp., Valencia, CA).  Poly(A)+ RNA was isolated using Oligotex (Qiagen Inc., Valencia, CA), and 4 mg of poly (A)+ RNA was used for each cDNA synthesis using Superscript II reverse transcriptase (Life Technologies, Carlsbad, CA).  cDNA was labeled using 100 mM Cy5-dUTP or Cy3-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ).  Excess nucleotides and primers were removed using QIAquick PCR Purification Kit (Qiagen, Valencia, CA).  About 95% of the spotted cDNAs showed significant hybridization when leaf mRNA was used for the experiments.  The control sample was labeled with Cy5-dUTP fluorescent dye and the UV treatment sample was labeled with Cy3-dUTP (Amersham Pharmacia Biotech, Piscataway, NJ, USA).  Two samples, one labeled with each dye, were mixed and then hybridized to a microarray for 15 h at 60°C.  The slides were washed in three wash steps: 2x SSC, 0.5% SDS; 0.5x SSC; and 0.05x SSC.  The three washes were at room temperature for 5 min each with gentle shaking.  The slides were scanned with a GenePix 4000B Scanner (Axon Instruments Inc., Union City, CA).  Normalization between the Cy3 and Cy5 fluorescent dye emission channels was achieved by adjusting the levels of both image intensities.  Scanalyze (Eisen, http://rana.lbl.gov/EisenSoftware.htm) was used to quantify the image files from the scanner.
Keywords = ultraviolet maize corn seedling leaf

organism: Zea mays

source_name: Mo17 seedling leaf2and3 ultraviolet treatment

source_name: Mo17 seedling leaf2and3 control


title: B73Ch1greenUV2

source_name: B73 seedling leaf2and3 ultraviolet treatment

source_name: B73 seedling leaf2and3 control